{ "cells": [ { "cell_type": "markdown", "metadata": { "colab_type": "text", "id": "Fedyc0IC4Sm1" }, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": { "colab_type": "text", "id": "mZ-gL5Vq4Sm7" }, "source": [ "\n", "< [Visualization and `pyrosetta.distributed.viewer`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) >

\"Open" ] }, { "cell_type": "markdown", "metadata": { "colab_type": "text", "id": "EV5XxB914SnD" }, "source": [ "# Rosetta Energy Score Functions" ] }, { "cell_type": "markdown", "metadata": { "colab_type": "text", "id": "pf_LH1wf4SnH" }, "source": [ "A basic function of Rosetta is calculating the energy or score of a biomolecule. Rosetta has a standard energy function for all-atom calculations as well as several scoring functions for low-resolution protein representations. See https://www.ncbi.nlm.nih.gov/pubmed/28430426 for a review on the all-atom score functions.\n", "\n", "You can also tailor an energy function by including scoring terms of your choice with custom weights." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Chapter contributors:**\n", "\n", "- Kathy Le (Johns Hopkins University) adapted this chapter from the [PyRosetta Workshops](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8) \n", " (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte, 2017)." ] }, { "cell_type": "markdown", "metadata": { "colab_type": "text", "id": "74AxDp8v4SnL" }, "source": [ "\n", "< [Visualization and `pyrosetta.distributed.viewer`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) >

\"Open" ] } ], "metadata": { "colab": { "name": "03.00-Rosetta-Energy-Score-Functions.ipynb", "provenance": [] }, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.0" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": false } }, "nbformat": 4, "nbformat_minor": 1 }